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Back to the Future of Soil Metagenomics

Joseph Nesme 1 Wafa Achouak 2, 3 Spiros N. Agathos 4 Mark Bailey 5 Petr Baldrian 6 Dominique Brunel 7 Asa Frostegard 8 Thierry Heulin 2, 3 Janet K. Jansson 9 Kristiina Kruus 10 George Kowalchuk 11 Antonio Lagares 12 Hilary Lappin-Scott 13 Philippe P. Lemanceau 14 Denis Le Paslier 15 Ines Mandic-Mulec 16 J. Colin Murrell 17 David Myrold 18 Renaud Nalin 19 Paolo Nannipieri 20 Josh Neufeld 21 Fergal O'Gara 22 John Parnell 23 Alfred Pühler 24 Victor Pylro 25 Juan Ramos 26 Luiz Roesch 25 Michael Schloter 27 Christa Schleper 28 Alexander Sczyrba 29 Angela Sessitsch 30 Sara Sjoling 31 Søren Sørensen 32 Christoph Tebbe 33 Edward Topp 34 George Tsiamis 35 Jan Dirk van Elsas 36 Geertje van Keulen 13 Franco Widmer 37 Michael Wagner 38 Tong Zhang 39 Xiaojun Zhang 1 Liping Zhao 40 Yong-Guan Zhu 41 Timothy M. Vogel 1 Pascal Simonet 1 
3 LEMIRE - Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes
BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) : DRF/BIAM
32 Section of Microbiology [Copenhagen]
Department of Biology [Copenhagen]
Abstract : Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?
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Joseph Nesme, Wafa Achouak, Spiros N. Agathos, Mark Bailey, Petr Baldrian, et al.. Back to the Future of Soil Metagenomics. Frontiers in Microbiology, 2016, 7, ⟨10.3389/fmicb.2016.00073⟩. ⟨hal-01923285⟩

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